Some comments and analysis from the exciting and fast moving world of Genomics. This blog focuses on next-generation sequencing and microarray technologies, although it is likely to go off on tangents from time-to-time

Pages

Wednesday, 14 November 2012

MiSeq: possible growth potential part 4

Our MiSeq has just been replaced after some performance issues and we are now getting ready to start running the upgraded version with the newest chemistry. Hopefully we'll be getting the 10Gb+ that Illumina reported some users are achieving.

In a GenomeWeb article yesterday Illumina responded to Life Technologies recent Proton updates (P1 80M, P2 4580M P3 1.2B sensors). MiSeq read lengths are increasing to 2x300bp and the number of reads will jump from 15-17M to 25M or more making 22Gb possible.

Way back in the Summer of 2011 I speculated that MiSeq would get to 25Gb by imaging more area and generating more reads (see MiSeq 1,), I have continued to follow the systems developments (see here, here and here) and am watching to see what else we might expect in the future. The MiSeq was sold as a box with a lot of potential locked down for easy upgrades and an 'Applesque' development path. Much of what has been made possible recently was probably available from launch, or at least considered by the designers.

Currently only one of the two "lanes" in the MiSeq is being imaged (imagine the return path as a separate lane). Further increases could come from bigger lanes or an upgrade to movable camera stage (unless there is one inside the box already). All pretty simple.

But how far does Illumina need to push MiSeq? With the 2500 rapid runs allowing the same degree of flexibility (on instrument clustering and 24 hour run times), any further increases to MiSeq make the GA dead-in-the-water. Perhaps Illumina will be driven by announcements by Life Technologies? Could Miseq ever deliver really fast run times like PGM or Proton? I'd say it does that already, a single-end 120bp run is completed in under 2 hours if you ignore clustering. Combined with Nextera genome prep you can get sample to genome in a working day.

So what should Illumina focus on next: My bet is that users will want the longest reads possible and we will learn to do new things with Sanger read lengths but tens of millions of them. Any de novo sequencing will be made much easier, structural variation is simplified and splicing becomes as trivial as differential gene expression by read counting (almost). And all of these could possibly be done with lower quality reads. Imagine a 100bp read with Q40 in the first and last 250bp, Q30 from 250-450 & 550-750 and Q10-20 in the middle?

2 comments:

We're finding that the increased read length has killed 454 and will most likely kill Ion Torrent. The only think stopping it is the diversity issue. Lots of people are wanting to sequence single (or a few) amplicons at really high depth across a number of patients/samples. For example to look at heterogeneity of tumor samples, or for 16S work. The PhiX spike-in is a messy work-around - who wants to lose 50% of their run to sequence a phage that has been sequenced to a astronomical depth already?!

Hi James, I was wondering if you could comment on the issues that led to your MiSeq being replaced? We have had a lot of problems with our MiSeq - new hard drive, three new reagent pumps, new mirror...

I met you a few years ago in Glasgow at an Illumina meeting but if you could email me I'd really appreciate it! Gavin dot Wilkie at glasgow dot ac dot uk

Over the last 16 years he's worked at; the Norfolk & Norwich Hospital on ErbB2, Royal London on Diabetes genetics, the Cambridge Uni Department of Pathology on Immunology group and the John Innes Centre on Wheat disease resistance gene cloning and arrays. In 2000 he set up an Affy and spotted microarray facility at JIC, he co-founded the UK Affy user group, which is still going strong. At JIC he also won a Biotech competition, and hopes one-day to start a business. Although none of his ideas have come to anything yet!

In 2006 James moved to set up the genomics facility at CRUK's new Cambridge Institute. Today the lab offers primarily NGS services on Illumina HiSeq, MiSeq & NextSeq for scientists at CRUK-CI and nine other University departments, as well as single-cell analysis on Fuildigm C1 and 10X Genomics.